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- EMDB-52420: CryoEM map of the large glutamate dehydrogenase composed of 180 k... -

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Basic information

Entry
Database: EMDB / ID: EMD-52420
TitleCryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Closed1 tetramer.
Map dataClosed 1 MsGDH tetramer map
Sample
  • Complex: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
    • Protein or peptide: NAD-specific glutamate dehydrogenase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
KeywordsLarge glutamate dehydrogenase / Tetramer / OXIDOREDUCTASE
Function / homology
Function and homology information


glutamate dehydrogenase / L-glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / L-aspartate:2-oxoglutarate aminotransferase activity
Similarity search - Function
NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain ...NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain / Glutamate dehydrogenase, helical motif 1 / Glutamate dehydrogenase, C-terminal / Glutamate dehydrogenase, ACT1 domain / Glutamate dehydrogenase, ACT2 domain / Glutamate dehydrogenase, ACT3 domain / Glutamate dehydrogenase, helical motif 3 / Glutamate dehydrogenase, helical motif 2 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsLazaro M / Chamorro N / Lopez-Alonso JP / Charro D / Rasia RM / Jimenez-Oses G / Valle M / Lisa MN
Funding support Spain, 1 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2021-124074NB-I00 Spain
CitationJournal: To Be Published
Title: Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase
Authors: Lazaro M / Chamorro N / Lopez-Alonso JP / Charro D / Rasia RM / Jimenez-Oses G / Valle M / Lisa MN
History
DepositionDec 23, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52420.png

Downloads & links

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Map

FileDownload / File: emd_52420.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClosed 1 MsGDH tetramer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 340 pix.
= 439.416 Å		1.29 Å/pix.
x 340 pix.
= 439.416 Å		1.29 Å/pix.
x 340 pix.
= 439.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.019422334 - 0.052641682
Average (Standard dev.)0.000048965307 (±0.0016037201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 439.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52420_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52420_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52420_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis...

EntireName: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
Components
  • Complex: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
    • Protein or peptide: NAD-specific glutamate dehydrogenase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis...

SupramoleculeName: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: MsLGDH180 tetramer in the closed1 conformation
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: strain ATCC 700084 / mc(2)155
Molecular weightTheoretical: 174 KDa

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Macromolecule #1: NAD-specific glutamate dehydrogenase

MacromoleculeName: NAD-specific glutamate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glutamate dehydrogenase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 176.341859 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHENL YFQGAASMIR RLSVAFLSTY RGPQADAPGV TSTGPLAVAA HDDLVSDDLV AAHYRLASMR APGETKAAVY PGDAGSGAA LQIVTDQAPM LVDSVTVLLH RHGIAYTAIM NPVFRVRRGL DGELLDVRPA AEAAPGDGAD ECWILVPITA A ADGEALTE ...String:
MHHHHHHENL YFQGAASMIR RLSVAFLSTY RGPQADAPGV TSTGPLAVAA HDDLVSDDLV AAHYRLASMR APGETKAAVY PGDAGSGAA LQIVTDQAPM LVDSVTVLLH RHGIAYTAIM NPVFRVRRGL DGELLDVRPA AEAAPGDGAD ECWILVPITA A ADGEALTE ATRLVPGILA EARQIGLDSG AMIAALHGLA NDLATDLEGH FPNAERKEVA ALLRWLADGH FVLLGYQQCV VG DGNAEVD PASRLGVLRL RNDVLPPLTD SDDLLVLAQA TMPSYLRYGA YPYIVVVRES PGASRVIEHR FVGLFTVAAM NAN ALEIPL ISRRVEEALA MAHRDPSHPG QLLRDIIQTI PRPELFALSS KQLLEMALAV VDLGSRRRTL LFLRADHLAH FVSC LVYLP RDRYTTAVRL EMQDILVREL GGAGIDYSAR VSESPWAVVH FTVRLPEGTA ADSVDTSLEN ESRIQDLLTE ATRNW GDRM ISAAAAASIS PAALEHYAHA FPEDYKQAFA PQDAIADISL IEALQDDSVK LVLADTAEDR VWKLTWYLGG HSASLS ELL PMLQSMGVVV LEERPFTLRR TDGLPVWIYQ FKISPHPSIP HAPDAEAQRD TAQRFADAVT AIWHGRVEID RFNELVM RA GLTWQQVVVL RAYAKYLRQA GFPYSQSHIE SVLNENPHTT RSLIDLFEAL FDPSQETDGR RDAQGAAAAV AADIDALV S LDTDRVLRAF ANLIEATLRT NYFVARPDSA RARNVLAFKL NPLVIKELPL PRPKFEIFVY SPRVEGVHLR FGFVARGGL RWSDRREDFR TEILGLVKAQ AVKNAVIVPV GAKGGFVVKR PPTLTGDAAA DREATRAEGV ECYRLFISGL LDVTDNVDKA TGAVVTPPE VVRRDGEDAY LVVAADKGTA TFSDIANEVA KSYGFWLGDA FASGGSIGYD HKAMGITAKG AWESVKRHFR E MGVDTQTQ DFTVVGIGDM SGDVFGNGML LSKHIRLVAA FDHRDIFLDP NPDAGRSWDE RKRLFDLPRS SWADYDKSLI SE GGGVYSR QQKSIPISPQ VRTALGLDAD VEELTPPALI KAILKAPVDL LWNGGIGTYI KAETEADADV GDRANDQIRV CGN QVRAKV IGEGGNLGVT ALGRIEFDLA GGRINTDALD NSAGVDCSDH EVNIKILIDS AVTAGKVTPE ERTELLLSMT DEVG ELVLA DNRDQNDLMG TSRANAASLL SVHARMIKDL VDNRGLNREL EALPSEKEIR RRADAGIGLT SPELATLMAH VKLAL KDDV LASDLPDQEV FASRLPYYFP TRLREELHGE IRSHQLRREI ITTMLVNDLV DTAGISYAYR ITEDVGVGPV DAVRSY VAI NAIFGIGDVW RRIRAAGDAG VPTSVTDRMT LDLRRLVDRA GRWLLNYRPQ PLAVGAEINR FGAKVAALTP RMSEWLR GD DKAIVSKEAG DFASHGVPED LAYHIATGLY QYSLLDVIDI ADIVDREPDE VADTYFALMD HLGADALLTA VSRLSRDD R WHSLARLAIR DDIYGSLRAL CFDVLAVGEP DENGEEKIAE WETTNSSRVT RARRTLTEIY KDGEQDLATL SVAARQIRS MTRTSGTGTT G

UniProtKB: NAD-specific glutamate dehydrogenase

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.125 mg/mL
BufferpH: 6.5
Component:
ConcentrationName
20.0 mMMES
300.0 mMNaCl
42.0 mMGlutamate
4.0 mMNAD
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

11606


Details: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation) at 4.19 A resolution
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 45998
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9huy:
CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Closed1 tetramer.

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